Labour Inspectorate construction sector strategy lead Jeanie Borsboom said deductions from wages must always be agreed to by the employee.
"It's not enough to have a deductions clause in the employment agreement," she said.
"Even then, the deductions must be reasonable. For example, employers cannot charge employees for operational costs that should be covered by the business."
"Employees who didn't agree to deductions or were pressured into agreeing can take a case to the ERA for as far back as six years."
The company did not engage with the Labour Inspectorate or participate in the ERA process.
It has also been placed on the Immigration Stand-down list, meaning it cannot hire any new migrant workers.
Borsboom said the workers had done the right thing in reporting it to the Philippines Embassy.
"Migrants are entitled to the same rights as New Zealand workers and the Inspectorate works closely with the embassy to ensure Filipino workers have access to information about their rights and are treated fairly in the workplace."
The Labour Inspectorate encouraged anyone concerned about an employment situation – either their own or someone else's - to contact the Ministry on 0800 20 90 20.